Thanks for taking the time to patching this. This works very well. And it doesn't mess with the part I am using colortbl for. I am accepting this as this answers my question but I have seen the wisdom of @egreg's advice about using aligned. Something's ought to break when things are not used properly. Just in this case, I did not know about it :)
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hpesoj626Dec 9 '12 at 11:34

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@hpesoj626 OTOH there is no reason to assume this shouldn't work. Everybody not experienced with the way LaTeX "programming" works would assume the \parbox is sufficient to "encapsulate" the align environment sufficiently from the influence of the tabular. It's a real disease of TeX's dynamic scoping and execution model that you get this kind of "overwrite" effect in almost every place where you nest things.
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Stephan LehmkeDec 9 '12 at 11:53

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Yes making colortbl mess with everycr was probably a mistake, it simplified the colortbl coding but makes it harder not to break nested alignments. I haven't really time to look today but the patch looks about right (or slower but possibly better) instead of patching align to reset everycr could get colortbl to reset it every cell so that any nested halign would work
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David CarlisleDec 9 '12 at 12:22